Comparing the stories, I think Mass Effect is as all about the main plot with cookie-cutter side-quests thrown in; FO3 is all about side-quests and involving exploration, its main quest far plainer than some side quests (Those! is my favourite).

I just finished FO3. An excellent game. But I wish the concept was closer to FO1&2, where you travel to varied communities, make decisions that influence their development and see how it all ties in together in the final narrative. It would be great to have multiple solutions (like in FO1's Cathedral and Stronghold), too. I guess it's too much wishful thinking .